pumpkin whoopie pies with cream cheese filling

It’s officially fall; the leaves are changing colors, the weather is cooling off, the smell of pumpkin cookies are in the air as I sit here writing. Ahhh, how I love fall. Last year, I had “Make Pumpkin Whoopie Pies” on my Fall Fun List and never got around to making them, so I thought I had better get them done early this year. I’m soooo glad I did. They are amazing and my whole family loves them. I have been handing them out with gift baskets that I have been making for friends.
Whenever I find a new recipe, I always follow the directions the first time I make it so I can see what it’s supposed to taste like. Then I start to play. I usually tweak one thing at a time, but I didn’t have time for that this year. I took a chance and made all my usual changes; messing with the flour (this recipe already called for whole wheat so I left it alone), the oil or fat, the eggs and the sugar. So here is my final result. My family like them even more than the original recipe and they are a little healthier. I left the cream cheese filling recipe alone; my husband forbids me to mess with it. So here is the recipe for Pumpkin Whoopie Pies with Cream Cheese Filling or as my three-year-old calls them, “Punkie Winkie Pies”.
Photo from Andrea Calvert
Photo from Andrea Calvert
Here is the amazing website where I found the original yummy recipe.
For cookies:
  • 3 cups organic whole white wheat flour OR 1.5 cups whole wheat while flour and 1.5 cups oat or almond flour (this gives it a little heartier texture)
  • 1 tsp salt
  • 1 tsp baking powder
  • 1 tsp baking soda
  • 2 tablespoons ground cinnamon
  • 2 tablespoons all spice (you can also use 1 tbsp. ground ginger and 1tbsp ground cloves)
  • 1 cup packed brown sugar
  • 3/4 cup maple syrup
  • 1/2 cup Organic Coconut Oil
  • 1/2 cup unsweetened applesauce
  • 1 1/2 cups pumpkin puree
  • 2 tablespoons organic Flaxseed egg replacer (grind 2 tbsp. of flaxseed in the Vitamix or blender and combine this with 6 tbsp. water)
  1. Combine flour, salt, baking powder, baking soda, cinnamon and allspice in a large bowl.
  2. In another bowl, beat together brown sugar, maple syrup, coconut oil, applesauce, pumpkin puree and flaxseed egg replacer.
  3. Combine wet ingredients into the dry ingredients, and blend together until fully mixed.
  4. Preheat the oven to 350 degrees Fahrenheit.
  5. Line cookie sheet with a Non-Stick Silicone Baking Mat or parchment paper. (I much prefer the baking mat. You don’t have to use cooking spray and the cookies never stick, they slide right off. Thanks to my sister, Michelle, I now use it for baking all of my cookies.)
  6. Drop approximately 1 tbsp size spoonful (for smaller-sized whoopie pies) onto the baking mat, about 2 inches apart. If you prefer them thinner, pat them down with a spoon into a rounded shape.
  7. Bake for 10-12 minutes, or until toothpick comes out clean. Remove from pan and place on a cooling rack.


For Filling: (you might need to make an additional half-recipe of the filling if you are like our family and require more filling in between your cookies)

  • 3 cups powdered sugar
  • 1 stick of softened butter
  • 8 ounces softened cream cheese
  • 1 teaspoon pure vanilla extract
  • 1/4 tsp cinnamon


  1. Beat together the cream cheese and butter with a mixer. Add in the powdered sugar, and beat until smooth. Add in the vanilla and cinnamon and blend well.
  2. When cookies are cooled, sandwich about 1 heaping tablespoon of cream cheese filling (or more) in between two comparable sized cookies (my kids love doing this for me). Slightly press and adjust so that the filling is even and to the edge of the whoopie pie.
  3. Refrigerate before serving if you would like the filling to firm up a bit, or serve warm with gooey frosting.


This recipe makes about 84 two-inch cookies which yields approximately 43 small whoopie pies.

I would love your suggestions on how to make this even healthier. Hope you enjoy!


6 thoughts on “pumpkin whoopie pies with cream cheese filling

  1. Heidi,
    These look so yummy. Can’t wait to try them!
    I am sure the best part of having them is the fun of watching the joy the children get from making as well as tasting them!!
    Ideas: When my son isn’t looking put some pumpkin and spice in the cream!!
    Some more healthy ideas.
    Add chopped, slightly toasted walnuts or pecans to the cookie mix.
    You could add Coconut to the cookies and or chopped dried cranberries, or maybe raisins.
    To ramp up the vegan direction make non dairy ice cream. Freeze it in an old plastic bottle. Cut the bottle off the ice cream roll and slice…quick put between cookies and eat.
    Not in the highly healthy category but these cookies would taste awesome with spiced cider.
    Oh my that led me to think of eating them with hot homemade applesauce. Now there you go for a HEALTHY upgrade!
    Thanks for delighting us with your fun blog!
    Love ya, mom Jan

    1. LOVE those ideas! Can’t wait to try them. I’m always happy to get ideas from a gourmet cook. Thanks for sharing them.

  2. I think I should sample one before attempting the recipe… Just so I know what the finished product is supposed to taste like!

  3. I love the ice cream idea! I make my own but never thought of doing that, thanks to Jan and Heidi

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